chr9-111943865-T-C

Variant names:

• chr9-111943865-T-C
• rs7863587
• XR_007061735.1:n.1093A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061735.1(LOC124902250):​n.1093A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,166 control chromosomes in the GnomAD database, including 1,886 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (1886 hom., cov: 32)
• Consequence: LOC124902250 XR_007061735.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 5 publications found

Genes affected

LOC124902250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902250	XR_007061735.1	n.1093A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23603 AN: 152048 Hom.: 1877 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.155 AC: 23643 AN: 152166 Hom.: 1886 Cov.: 32 AF XY: 0.155 AC XY: 11506 AN XY: 74392

African (AFR) AF: 0.165 AC: 6831 AN: 41490

American (AMR) AF: 0.112 AC: 1707 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3466

East Asian (EAS) AF: 0.0929 AC: 481 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1635 AN: 10594

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10734 AN: 68012

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.163 Hom.: 1166

Bravo AF: 0.150

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.31
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7863587; hg19: chr9-114706145;